The impact of transposable elements in adaptive evolution

<jats:title>Abstract</jats:title> <jats:p> The growing knowledge about the influence of transposable elements ( <jats:styled-content style="fixed-case">TE</jats:styled-content> s) on (a) long‐term genome and transcriptome evolution; (b) genomic, transcriptomic and epigenetic variation within populations; and (c) patterns of somatic genetic differences in individuals continues to spur the interest of evolutionary biologists in the role of <jats:styled-content style="fixed-case">TE</jats:styled-content> s in adaptive evolution. As <jats:styled-content style="fixed-case">TE</jats:styled-content> s can trigger a broad range of molecular variation in a population with potentially severe fitness and phenotypic consequences for individuals, different mechanisms evolved to keep <jats:styled-content style="fixed-case">TE</jats:styled-content> activity in check, allowing for a dynamic interplay between the host, its <jats:styled-content style="fixed-case">TE</jats:styled-content> s and the environment in evolution. Here, we review evidence for adaptive phenotypic changes associated with <jats:styled-content style="fixed-case">TE</jats:styled-content> s and the basic molecular mechanisms by which the underlying genetic changes arise: (a) domestication, (b) exaptation, (c) host gene regulation, (d) <jats:styled-content style="fixed-case">TE</jats:styled-content> ‐mediated formation of intronless gene copies—so‐called retrogenes and (e) overall increased genome plasticity. Furthermore, we review and discuss how the stress‐dependent incapacitation of defence mechanisms against the activity of <jats:styled-content style="fixed-case">TE</jats:styled-content> s might facilitate adaptive responses to environmental challenges and how such mechanisms might be particularly relevant in species frequently facing novel environments, such as invasive, pathogenic or parasitic species. </jats:p>